1) 18S amplicons

1.1) Data overview

The dataset “Malaspina 18S iTags” contains reads from 122 samples of Malaspina. On average, each sample contains 126100 OTUs:

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    4050   59560   98630  126100  157000  935800


Overall reads per sample:

1.2) Normalization


In order to keep as many samples as possible, we rarefy at 49975 reads per sample. By that, we loose 31 samples, and after removing the exluded samples in the 16S dataset (to make them comparable), we end up with a normalized dataset containing 43 samples and 5669 OTUs.

tb18_tax_occur_min49975_t<-t(tb18_tax_occur_min49975)
tb18_tax_occur_ss49975<-rrarefy(tb18_tax_occur_min49975_t, 49975)

The normalized table shows the following dimensions and format:

## [1]    91 43734
##              OTU_2 OTU_106 OTU_403 OTU_139 OTU_4
## st055_MD1013  8998     718      80     104   225
## st057_MD1042  2642     241      45      29   121
## st058_MD1080  1305     866       3      17    46
## st059_MD1100   423     705      12      33   182
## st009_MD111   2212       8       0      60    94

Its content fits with the expected normalization values (49975 reads per station):

rowSums(tb18_tax_occur_ss49975)
##  st055_MD1013  st057_MD1042  st058_MD1080  st059_MD1100   st009_MD111 
##         49975         49975         49975         49975         49975 
##  st060_MD1125  st062_MD1143  st065_MD1209  st066_MD1222 st068b_MD1260 
##         49975         49975         49975         49975         49975 
##  st069_MD1293  st070_MD1302  st072_MD1331  st073_MD1354  st074_MD1368 
##         49975         49975         49975         49975         49975 
##  st075_MD1398   st010_MD141  st076_MD1421  st077_MD1425  st078_MD1459 
##         49975         49975         49975         49975         49975 
##  st079_MD1475  st081_MD1479  st082_MD1490  st085_MD1537  st086_MD1559 
##         49975         49975         49975         49975         49975 
##  st087_MD1589  st088_MD1607  st089_MD1629  st092_MD1672  st093_MD1700 
##         49975         49975         49975         49975         49975 
##  st094_MD1724  st095_MD1744  st096_MD1772  st097_MD1798  st098_MD1811 
##         49975         49975         49975         49975         49975 
##  st101_MD1857  st102_MD1885  st103_MD1887  st104_MD1928  st106_MD1956 
##         49975         49975         49975         49975         49975 
##  st107_MD1964   st012_MD196  st108_MD2004  st109_MD2008  st110_MD2047 
##         49975         49975         49975         49975         49975 
##  st112_MD2051  st114_MD2094  st115_MD2111   st014_MD214  st118_MD2155 
##         49975         49975         49975         49975         49975 
##  st120_MD2243  st126_MD2380  st127_MD2408  st128_MD2436  st129_MD2448 
##         49975         49975         49975         49975         49975 
##  st131_MD2516   st015_MD254  st132_MD2562  st133_MD2594   st017_MD266 
##         49975         49975         49975         49975         49975 
##  st138_MD2723  st140_MD2761   st018_MD285  st143_MD2864    st001_MD28 
##         49975         49975         49975         49975         49975 
##  st145_MD2956   st019_MD311   st022_MD346   st023_MD366   st024_MD389 
##         49975         49975         49975         49975         49975 
##    st002_MD40   st025_MD417   st026_MD439   st027_MD458   st028_MD486 
##         49975         49975         49975         49975         49975 
##    st003_MD52   st032_MD550   st033_MD575   st034_MD591    st005_MD64 
##         49975         49975         49975         49975         49975 
##   st038_MD664   st039_MD684   st040_MD712   st041_MD734   st043_MD753 
##         49975         49975         49975         49975         49975 
##   st044_MD778   st045_MD806   st047_MD854   st049_MD876   st050_MD897 
##         49975         49975         49975         49975         49975 
##   st052_MD940 
##         49975

Let’s check out how many OTUs don’t appear in the new table:

length(which(colSums(tb18_tax_occur_ss49975)==0)) #8045
## [1] 5323

There are 8045 OTUs that don’t show any occurrence in the normalized data. Let’s remove them from the table and take a look at its final dimensions:

tb18_tax_occur_ss49975_no_cero<-tb18_tax_occur_ss49975[,-(which(colSums(tb18_tax_occur_ss49975)==0))]
tb18_tax_occur_ss49975_no_cero<-tb18_tax_occur_ss49975_no_cero[mixedorder(row.names(tb18_tax_occur_ss49975_no_cero)),]
dim(tb18_tax_occur_ss49975_no_cero) #91 38645
## [1]    91 38411

Datasets summary:

dim(tb18_tax) #46690   129
## [1] 46690   129
dim(tb18_tax_occur) #46690   122
## [1] 46690   122
dim(tb18_tax_occur_ss49975_no_cero) #91 38645
## [1]    91 38411

1.3) General community analysis

1.3.1) Richness and evenness (Shannon index)

Most of the samples take Shannon Index values around 6:

1.3.2) Richness: OTU number

Lowest number of OTUs per sample:

## [1] 1268

Maximum number of OTUs per sample:

## [1] 5187

In most of the samples, we can identify between 600 and 700 OTUs:

1.3.3) Index of evenness

1.3.3.1) Pielou’s index

The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Most of the samples get values between 0.90 and 0.95, meaning that the numerical composition of different OTUs in a sample is highly variable - there’s no constant presence of dominant species. ’

1.3.4) Abundance Models

Most of the OTUs show very few occurrences, suggesting that we will probably be able to identify a significant ammount of rare otus:

1.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)

The OTUs abundance distribution fits relativelly close to log-normal model.

1.3.4.2) Preston’s Log-normal Model

According to Preston’s lognormal model fitted into groups of species’ frequencies, we’re missing 1588.816 species: ’

## Extrapolated     Observed       Veiled 
##    46340.804    43734.000     2606.804


When computing Prestons’ lognormal model fit without pooling data into groups, we miss 1385.371 species: ’

## Extrapolated     Observed       Veiled 
##    46197.162    43734.000     2463.162

1.3.5) Rarefaction curves of rarefied and non-rarefied datasets

1.3.6) Beta diversity

1.3.6.1) Dissimilarity matrix using Bray-Curtis index:

The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and the relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values around 0.8, meaning that their composition is substantially different.

1.3.6.2) Hierarchical clustering

The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups, apart from the one containing TARA_84, TARA_82 and TARA_85.

(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)

1.3.6.3) Non-metric multidimensional scaling

We can identify a prominent group in the central part of the NMDS plot and a few outliers (TARA 82, 84 and 85) in the central-right edge of the plot. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.

## 
## Call:
## monoMDS(dist = tb18_tax_occur_ss49975_no_cero.bray) 
## 
## Non-metric Multidimensional Scaling
## 
## 91 points, dissimilarity 'bray', call 'vegdist(x = tb18_tax_occur_ss49975_no_cero, method = "bray")'
## 
## Dimensions: 2 
## Stress:     0.2055046 
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 120 iterations: Stress nearly unchanged (ratio > sratmax)

1.4) Geographical analysis

## Warning in if (class(lats) == "SpatialPoints") lats <- coordinates(lats):
## the condition has length > 1 and only the first element will be used

Working datasets:

  1. Community matrix: tb18_tax_occur_ss49975_no_cero
dim(tb18_tax_occur_ss49975_no_cero)
## [1]    91 38411
tb18_tax_occur_ss49975_no_cero[1:5, 1:5]
##             OTU_2 OTU_106 OTU_403 OTU_139 OTU_4
## st001_MD28    154      35       0       4    44
## st002_MD40    249       8      10       6    45
## st003_MD52    733      21      41      15    32
## st005_MD64    847      97      11       0   125
## st009_MD111  2212       8       0      60    94
  1. Community Bray-Curtis: tb18_tax_occur_ss49975_no_cero.bray
dim(tb18_tax_occur_ss49975_no_cero.bray)
## [1] 91 91
  1. Stations distances in km: geo_distances_MP_18S
dim(geo_distances_MP_18S)
## [1] 91 91

Communities quickly change their composition across geographical distances:

plot(geo_distances_MP_18S, tb18_tax_occur_ss49975_no_cero.bray, pch=19, cex=0.4, xlab="Geopgraphical distances", ylab="Bray-Curtis dissimilarities")

1.4.1) Mantel correlograms

Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.

mantel(geo_distances_MP_18S, tb18_tax_occur_ss49975_no_cero.bray)
## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## mantel(xdis = geo_distances_MP_18S, ydis = tb18_tax_occur_ss49975_no_cero.bray) 
## 
## Mantel statistic r: 0.1713 
##       Significance: 0.001 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0208 0.0277 0.0326 0.0378 
## Permutation: free
## Number of permutations: 999

Maximum distance between samples:

## [1] 19500.19

Minimum distance between samples:

## [1] 0

Correlograms:

MP_18s_ss49975_mantel_correl_by_1000km<-mantel.correlog(tb18_tax_occur_ss49975_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=1000))
plot(MP_18s_ss49975_mantel_correl_by_1000km)

MP_18s_ss49975_mantel_correl_by_100km<-mantel.correlog(tb18_tax_occur_ss49975_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=100))
plot(MP_18s_ss49975_mantel_correl_by_100km)

1.5) Abundance vs. occurence

In the following plot, we can appreciate the OTUs distribution according to their percentage of occurence and relative abundance. The red line keeps up OTUs that occur in more than 80% of the samples, the green line limits regionally rare OTUs (< 0.001%), and the blue one restricts regionally abundant OTUs (> 0.1%).

Regionally abundant OTUs (relative abundance over 0.1%):

tb18_ss49975_abundant_sorted_prov<-cbind(otu_names=row.names(tb18_ss49975_abundant_sorted),tb18_ss49975_abundant_sorted)
##     otu_names mean_rabund perc_occur SILVA_plus_MAS_plus_BM_classif
## 1       OTU_1 0.008781754  100.00000                    Dinophyceae
## 2      OTU_10 0.004581192   92.30769                           <NA>
## 3     OTU_100 0.001011275   68.13187                           <NA>
## 4     OTU_101 0.002365139   85.71429                           <NA>
## 5     OTU_102 0.001926458   80.21978                           <NA>
## 6   OTU_10246 0.001132434   73.62637                           <NA>
## 7     OTU_103 0.001537692   90.10989                           <NA>
## 8     OTU_104 0.001532195   80.21978                           <NA>
## 9     OTU_105 0.001428626   49.45055                           <NA>
## 10    OTU_106 0.003967478   87.91209                           <NA>
## 11    OTU_108 0.001561220   72.52747                           <NA>
## 12    OTU_109 0.001797602   68.13187                           <NA>
## 13     OTU_11 0.007027030  100.00000                           <NA>
## 14    OTU_110 0.001648736   85.71429                    Dinophyceae
## 15    OTU_111 0.001400261   93.40659                    Dinophyceae
## 16    OTU_112 0.001392564   94.50549                    Dinophyceae
## 17    OTU_113 0.001131995   72.52747                           <NA>
## 18   OTU_1136 0.001319561   98.90110                    Dinophyceae
## 19  OTU_11454 0.001878742  100.00000                           <NA>
## 20    OTU_115 0.001262389   46.15385                           <NA>
## 21    OTU_116 0.001794744   83.51648                           <NA>
## 22    OTU_117 0.001035463   91.20879                           <NA>
## 23    OTU_118 0.001049096   70.32967                           <NA>
## 24  OTU_11833 0.001184988   84.61538                           <NA>
## 25    OTU_119 0.002803160   29.67033                           <NA>
## 26     OTU_12 0.008681264  100.00000                           <NA>
## 27    OTU_120 0.001065148   69.23077                           <NA>
## 28    OTU_121 0.001660611   98.90110                    Dinophyceae
## 29    OTU_122 0.001206757   64.83516                           <NA>
## 30    OTU_123 0.001049316   75.82418                           <NA>
## 31    OTU_124 0.001658851   85.71429                           <NA>
## 32    OTU_125 0.001231165   96.70330                           <NA>
## 33    OTU_126 0.001683039   96.70330                           <NA>
## 34    OTU_128 0.001140131   85.71429                           <NA>
## 35    OTU_129 0.001122100   68.13187                  Chrysophyceae
## 36     OTU_13 0.007213057   98.90110                           <NA>
## 37    OTU_130 0.001101650   98.90110                           <NA>
## 38    OTU_131 0.001242819   96.70330               Dictyochophyceae
## 39    OTU_132 0.001200600   58.24176                           <NA>
## 40    OTU_133 0.001020510   58.24176                           <NA>
## 41    OTU_135 0.001377832   89.01099                  Chrysophyceae
## 42    OTU_136 0.001136832   52.74725                           <NA>
## 43    OTU_137 0.002192965   60.43956                           <NA>
## 44     OTU_14 0.003648857   92.30769                           <NA>
## 45    OTU_140 0.001131115   80.21978                           <NA>
## 46    OTU_141 0.001076802   68.13187                           <NA>
## 47    OTU_142 0.001212474   73.62637        Prasinophyceae_clade-IX
## 48    OTU_144 0.001016552   91.20879                           <NA>
## 49    OTU_145 0.001233364   90.10989                           <NA>
## 50    OTU_146 0.001207197   68.13187                           <NA>
## 51  OTU_14696 0.006999324   96.70330                           <NA>
## 52     OTU_15 0.003874904   52.74725                           <NA>
## 53    OTU_151 0.001051295   69.23077                  Chrysophyceae
## 54    OTU_157 0.001029966   45.05495                           <NA>
## 55     OTU_16 0.002029146   37.36264       Prasinophyceae_clade-VII
## 56    OTU_161 0.001166078   57.14286                           <NA>
## 57    OTU_162 0.001254254   78.02198                           <NA>
## 58    OTU_163 0.001052174   76.92308                           <NA>
## 59    OTU_165 0.001165198   79.12088                           <NA>
## 60     OTU_17 0.004120962   94.50549                           <NA>
## 61    OTU_174 0.001125618   73.62637                           <NA>
## 62    OTU_177 0.001247437   93.40659                           <NA>
## 63    OTU_179 0.001122759   76.92308                           <NA>
## 64     OTU_18 0.006851118  100.00000                    Dinophyceae
## 65    OTU_180 0.001235783   70.32967                           <NA>
## 66   OTU_1819 0.001154203   68.13187                           <NA>
## 67   OTU_1842 0.001043819   95.60440                    Dinophyceae
## 68    OTU_188 0.001347927   96.70330                    Dinophyceae
## 69   OTU_1882 0.001431925   68.13187                           <NA>
## 70     OTU_19 0.004458713  100.00000                           <NA>
## 71    OTU_192 0.001203019   96.70330                           <NA>
## 72      OTU_2 0.035255650  100.00000                           <NA>
## 73     OTU_20 0.007444821   56.04396                  Pelagophyceae
## 74     OTU_21 0.005340692   94.50549                           <NA>
## 75     OTU_22 0.004716644   90.10989                           <NA>
## 76    OTU_220 0.001011495   96.70330                           <NA>
## 77     OTU_23 0.012380256   96.70330                           <NA>
## 78    OTU_235 0.001181250   87.91209                           <NA>
## 79     OTU_24 0.006635186   98.90110                           <NA>
## 80    OTU_243 0.001311205   97.80220                           <NA>
## 81     OTU_25 0.010682484  100.00000                    Dinophyceae
## 82     OTU_26 0.005086719   96.70330                           <NA>
## 83     OTU_27 0.010048541  100.00000                           <NA>
## 84     OTU_28 0.004053675   94.50549                           <NA>
## 85     OTU_29 0.002486298   98.90110                           <NA>
## 86      OTU_3 0.005880523   85.71429                           <NA>
## 87     OTU_30 0.003450297   75.82418                           <NA>
## 88     OTU_31 0.003347388   95.60440                           <NA>
## 89     OTU_32 0.002116003   79.12088                           <NA>
## 90     OTU_33 0.003162021   98.90110                    Dinophyceae
## 91    OTU_338 0.001067127   95.60440                    Dinophyceae
## 92     OTU_34 0.005884041   71.42857                  Chrysophyceae
## 93     OTU_35 0.002532475   87.91209                           <NA>
## 94  OTU_35494 0.001214893   67.03297                           <NA>
## 95  OTU_35799 0.002920141  100.00000                    Dinophyceae
## 96     OTU_36 0.003698772   89.01099                           <NA>
## 97     OTU_37 0.002797663   95.60440                           <NA>
## 98     OTU_38 0.003267128   92.30769                           <NA>
## 99     OTU_39 0.003175434   98.90110                    Dinophyceae
## 100  OTU_3988 0.001439181   78.02198                           <NA>
## 101     OTU_4 0.007494736  100.00000                    Dinophyceae
## 102    OTU_40 0.004197483  100.00000                    Dinophyceae
## 103    OTU_41 0.002807778   93.40659                           <NA>
## 104    OTU_42 0.002780731   95.60440                           <NA>
## 105    OTU_43 0.002653635   69.23077                           <NA>
## 106    OTU_44 0.004382191   46.15385                 Prasinophyceae
## 107    OTU_45 0.004615934  100.00000                    Dinophyceae
## 108    OTU_46 0.002691676   29.67033                 Prasinophyceae
## 109    OTU_47 0.003144869   75.82418                           <NA>
## 110    OTU_48 0.002605918   93.40659                           <NA>
## 111    OTU_49 0.002907608   98.90110                    Dinophyceae
## 112     OTU_5 0.004870567   80.21978                           <NA>
## 113    OTU_50 0.003971876   96.70330                           <NA>
## 114    OTU_51 0.003265369   89.01099                           <NA>
## 115    OTU_52 0.002850436   84.61538                           <NA>
## 116    OTU_53 0.002072245   39.56044                           <NA>
## 117    OTU_54 0.001937672   94.50549                           <NA>
## 118    OTU_55 0.003479102  100.00000                           <NA>
## 119    OTU_56 0.002308407   61.53846                           <NA>
## 120  OTU_5618 0.003488338   94.50549                           <NA>
## 121    OTU_57 0.001643679   93.40659                           <NA>
## 122    OTU_58 0.002871985   70.32967                           <NA>
## 123    OTU_59 0.001691175   79.12088                           <NA>
## 124     OTU_6 0.037113722  100.00000                           <NA>
## 125    OTU_61 0.001699751   82.41758                           <NA>
## 126    OTU_62 0.002200881   82.41758                           <NA>
## 127    OTU_63 0.001261070   51.64835       Prasinophyceae_clade-VII
## 128  OTU_6315 0.002216713   92.30769                           <NA>
## 129    OTU_64 0.003793985  100.00000                           <NA>
## 130    OTU_65 0.002952905   98.90110                           <NA>
## 131    OTU_66 0.002519502   97.80220                    Dinophyceae
## 132    OTU_67 0.001730975   96.70330                    Dinophyceae
## 133    OTU_68 0.002455953   96.70330                           <NA>
## 134    OTU_69 0.002547867   57.14286                           <NA>
## 135     OTU_7 0.008052598  100.00000                           <NA>
## 136    OTU_70 0.003676564   76.92308                           <NA>
## 137    OTU_71 0.002642200  100.00000                           <NA>
## 138    OTU_72 0.003091436   98.90110                           <NA>
## 139    OTU_73 0.002135573   72.52747                           <NA>
## 140    OTU_74 0.002443859   95.60440                           <NA>
## 141    OTU_75 0.002588767   97.80220                           <NA>
## 142    OTU_76 0.001810136   90.10989                           <NA>
## 143   OTU_767 0.001113084   28.57143                           <NA>
## 144    OTU_77 0.001463149   68.13187                    Dinophyceae
## 145    OTU_78 0.002187907  100.00000                    Dinophyceae
## 146  OTU_7889 0.002273225   86.81319                           <NA>
## 147     OTU_8 0.011284543   98.90110                           <NA>
## 148    OTU_80 0.002294774   70.32967                           <NA>
## 149    OTU_81 0.003532316   98.90110                           <NA>
## 150    OTU_82 0.002167237   89.01099                           <NA>
## 151    OTU_83 0.001595083   72.52747                           <NA>
## 152    OTU_84 0.003011616   74.72527                           <NA>
## 153    OTU_85 0.002143050   92.30769                           <NA>
## 154    OTU_87 0.001965598   92.30769               Dictyochophyceae
## 155    OTU_88 0.001378491   92.30769                           <NA>
## 156    OTU_89 0.002038382   71.42857                           <NA>
## 157  OTU_8924 0.001059651   71.42857                           <NA>
## 158     OTU_9 0.007790928   73.62637                           <NA>
## 159    OTU_90 0.001698432   96.70330                           <NA>
## 160    OTU_91 0.001143649   63.73626                           <NA>
## 161    OTU_92 0.002018372   75.82418                           <NA>
## 162    OTU_93 0.001216872   91.20879                           <NA>
## 163    OTU_94 0.001314943   94.50549                           <NA>
## 164    OTU_95 0.001584529   84.61538                           <NA>
## 165    OTU_96 0.002072905   65.93407                           <NA>
## 166    OTU_98 0.001593984   85.71429                           <NA>
## 167    OTU_99 0.001284818   69.23077                           <NA>
## [1] 167   4

Proportion of regionally abundant OTUs (%):

## [1] 0.4347713

Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):

otu_tb18_ss49975_cosmop_sorted_prov<-merge(otu_tb18_ss49975_cosmop_sorted_prov,tb18_class_prov, by="otu_names", all.x=TRUE)
##     otu_names mean_rabund perc_occur SILVA_plus_MAS_plus_BM_classif
## 1       OTU_1 0.008781754  100.00000                    Dinophyceae
## 2      OTU_10 0.004581192   92.30769                           <NA>
## 3     OTU_101 0.002365139   85.71429                           <NA>
## 4     OTU_102 0.001926458   80.21978                           <NA>
## 5     OTU_103 0.001537692   90.10989                           <NA>
## 6     OTU_104 0.001532195   80.21978                           <NA>
## 7     OTU_106 0.003967478   87.91209                           <NA>
## 8      OTU_11 0.007027030  100.00000                           <NA>
## 9     OTU_110 0.001648736   85.71429                    Dinophyceae
## 10    OTU_111 0.001400261   93.40659                    Dinophyceae
## 11    OTU_112 0.001392564   94.50549                    Dinophyceae
## 12   OTU_1136 0.001319561   98.90110                    Dinophyceae
## 13  OTU_11454 0.001878742  100.00000                           <NA>
## 14    OTU_116 0.001794744   83.51648                           <NA>
## 15    OTU_117 0.001035463   91.20879                           <NA>
## 16  OTU_11833 0.001184988   84.61538                           <NA>
## 17     OTU_12 0.008681264  100.00000                           <NA>
## 18    OTU_121 0.001660611   98.90110                    Dinophyceae
## 19    OTU_124 0.001658851   85.71429                           <NA>
## 20    OTU_125 0.001231165   96.70330                           <NA>
## 21    OTU_126 0.001683039   96.70330                           <NA>
## 22    OTU_128 0.001140131   85.71429                           <NA>
## 23     OTU_13 0.007213057   98.90110                           <NA>
## 24    OTU_130 0.001101650   98.90110                           <NA>
## 25    OTU_131 0.001242819   96.70330               Dictyochophyceae
## 26    OTU_135 0.001377832   89.01099                  Chrysophyceae
## 27     OTU_14 0.003648857   92.30769                           <NA>
## 28    OTU_140 0.001131115   80.21978                           <NA>
## 29    OTU_144 0.001016552   91.20879                           <NA>
## 30    OTU_145 0.001233364   90.10989                           <NA>
## 31  OTU_14696 0.006999324   96.70330                           <NA>
## 32     OTU_17 0.004120962   94.50549                           <NA>
## 33    OTU_177 0.001247437   93.40659                           <NA>
## 34     OTU_18 0.006851118  100.00000                    Dinophyceae
## 35   OTU_1842 0.001043819   95.60440                    Dinophyceae
## 36    OTU_188 0.001347927   96.70330                    Dinophyceae
## 37     OTU_19 0.004458713  100.00000                           <NA>
## 38    OTU_192 0.001203019   96.70330                           <NA>
## 39      OTU_2 0.035255650  100.00000                           <NA>
## 40     OTU_21 0.005340692   94.50549                           <NA>
## 41     OTU_22 0.004716644   90.10989                           <NA>
## 42    OTU_220 0.001011495   96.70330                           <NA>
## 43     OTU_23 0.012380256   96.70330                           <NA>
## 44    OTU_235 0.001181250   87.91209                           <NA>
## 45     OTU_24 0.006635186   98.90110                           <NA>
## 46    OTU_243 0.001311205   97.80220                           <NA>
## 47     OTU_25 0.010682484  100.00000                    Dinophyceae
## 48     OTU_26 0.005086719   96.70330                           <NA>
## 49     OTU_27 0.010048541  100.00000                           <NA>
## 50     OTU_28 0.004053675   94.50549                           <NA>
## 51     OTU_29 0.002486298   98.90110                           <NA>
## 52      OTU_3 0.005880523   85.71429                           <NA>
## 53     OTU_31 0.003347388   95.60440                           <NA>
## 54     OTU_33 0.003162021   98.90110                    Dinophyceae
## 55    OTU_338 0.001067127   95.60440                    Dinophyceae
## 56     OTU_35 0.002532475   87.91209                           <NA>
## 57  OTU_35799 0.002920141  100.00000                    Dinophyceae
## 58     OTU_36 0.003698772   89.01099                           <NA>
## 59     OTU_37 0.002797663   95.60440                           <NA>
## 60     OTU_38 0.003267128   92.30769                           <NA>
## 61     OTU_39 0.003175434   98.90110                    Dinophyceae
## 62      OTU_4 0.007494736  100.00000                    Dinophyceae
## 63     OTU_40 0.004197483  100.00000                    Dinophyceae
## 64     OTU_41 0.002807778   93.40659                           <NA>
## 65     OTU_42 0.002780731   95.60440                           <NA>
## 66     OTU_45 0.004615934  100.00000                    Dinophyceae
## 67     OTU_48 0.002605918   93.40659                           <NA>
## 68     OTU_49 0.002907608   98.90110                    Dinophyceae
## 69      OTU_5 0.004870567   80.21978                           <NA>
## 70     OTU_50 0.003971876   96.70330                           <NA>
## 71     OTU_51 0.003265369   89.01099                           <NA>
## 72     OTU_52 0.002850436   84.61538                           <NA>
## 73     OTU_54 0.001937672   94.50549                           <NA>
## 74     OTU_55 0.003479102  100.00000                           <NA>
## 75   OTU_5618 0.003488338   94.50549                           <NA>
## 76     OTU_57 0.001643679   93.40659                           <NA>
## 77      OTU_6 0.037113722  100.00000                           <NA>
## 78     OTU_61 0.001699751   82.41758                           <NA>
## 79     OTU_62 0.002200881   82.41758                           <NA>
## 80   OTU_6315 0.002216713   92.30769                           <NA>
## 81     OTU_64 0.003793985  100.00000                           <NA>
## 82     OTU_65 0.002952905   98.90110                           <NA>
## 83     OTU_66 0.002519502   97.80220                    Dinophyceae
## 84     OTU_67 0.001730975   96.70330                    Dinophyceae
## 85     OTU_68 0.002455953   96.70330                           <NA>
## 86      OTU_7 0.008052598  100.00000                           <NA>
## 87     OTU_71 0.002642200  100.00000                           <NA>
## 88     OTU_72 0.003091436   98.90110                           <NA>
## 89     OTU_74 0.002443859   95.60440                           <NA>
## 90     OTU_75 0.002588767   97.80220                           <NA>
## 91     OTU_76 0.001810136   90.10989                           <NA>
## 92     OTU_78 0.002187907  100.00000                    Dinophyceae
## 93   OTU_7889 0.002273225   86.81319                           <NA>
## 94      OTU_8 0.011284543   98.90110                           <NA>
## 95     OTU_81 0.003532316   98.90110                           <NA>
## 96     OTU_82 0.002167237   89.01099                           <NA>
## 97     OTU_85 0.002143050   92.30769                           <NA>
## 98     OTU_87 0.001965598   92.30769               Dictyochophyceae
## 99     OTU_88 0.001378491   92.30769                           <NA>
## 100    OTU_90 0.001698432   96.70330                           <NA>
## 101    OTU_93 0.001216872   91.20879                           <NA>
## 102    OTU_94 0.001314943   94.50549                           <NA>
## 103    OTU_95 0.001584529   84.61538                           <NA>
## 104    OTU_98 0.001593984   85.71429                           <NA>
## [1] 104   4

Number and proportion (%) of cosmopolitan OTUs:

## [1] 104
## [1] 0.2707558

Number and proportion (%) of rare OTUs:

nrow(otu_tb18_ss49975_rabund_percoccur[otu_tb18_ss49975_rabund_percoccur$mean_rabund < 0.00001 & otu_tb18_ss49975_rabund_percoccur$mean_rabund >0,])
## [1] 32696
## [1] 85.12145

1.6) Taxonomic composition analysis

1.6.1) Normalized data


PHOTOTROPHS + HETEROTROPHS

No. of OTUs and reads of the rearefied dataset:

## [1] 38411
## [1] 4547725


Number and proportion (%) of OTUs of phototrophic groups:

## [1] 11850
## [1] 30.85054

Number and proportion (%) of reads of phototrophic groups:

## [1] 950856
## [1] 20.90839


Number and proportion (%) of OTUs of non-phototrophic groups:

## [1] 26561
## [1] 69.14946

Number and proportion (%) of reads of non-phototrophic groups:

## [1] 3596869
## [1] 79.09161


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
##                                       59              1                NA
## Bacillariophyceae                   3636             98                88
## Bolidophyceae                       2971             15                89
## Chlorarachniophyceae                3335             70                89
## Chrysophyceae                      79873            361                91
## Cryptophyceae                       9910             77                80
## Dictyochophyceae                   39444            237                91
## Dinophyceae                       650673           9894                91
## Eustigmatales                        232              9                NA
## Heterotrophs                     3596869          26561                91
## MOCH-1                              4357             70                NA
## MOCH-2                             17109            131                NA
## MOCH-5                              2431             19                NA
## Mamiellophyceae                      340             32                41
## Pelagophyceae                      46796            339                90
## Pinguiophyceae                      1544             19                86
## Prasinophyceae                     51033            191                NA
## Prasinophyceae_clade-IX            11979             79                87
## Prasinophyceae_clade-VII           23960            125                87
## Prymnesiophyceae                     399             62                76
## Pyramimonadaceae                     113              3                 7
## Raphydophyceae                       211              4                51
## Trebouxiophyceae                     103              3                 4
## Ulvophyceae                           16              3                 4
## other_Prasinophyceae                 332              8                54


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##               100               100                NA
##                          reads_per_class OTUs_per_class samples_per_class
##                             1.297352e-03    0.002603421                NA
## Bacillariophyceae           7.995206e-02    0.255135248         96.703297
## Bolidophyceae               6.532937e-02    0.039051313         97.802198
## Chlorarachniophyceae        7.333337e-02    0.182239463         97.802198
## Chrysophyceae               1.756329e+00    0.939834943        100.000000
## Cryptophyceae               2.179112e-01    0.200463409         87.912088
## Dictyochophyceae            8.673348e-01    0.617010752        100.000000
## Dinophyceae                 1.430766e+01   25.758246336        100.000000
## Eustigmatales               5.101452e-03    0.023430788                NA
## Heterotrophs                7.909161e+01   69.149462394        100.000000
## MOCH-1                      9.580614e-02    0.182239463                NA
## MOCH-2                      3.762101e-01    0.341048137                NA
## MOCH-5                      5.345530e-02    0.049464997                NA
## Mamiellophyceae             7.476266e-03    0.083309469         45.054945
## Pelagophyceae               1.028998e+00    0.882559683         98.901099
## Pinguiophyceae              3.395104e-02    0.049464997         94.505495
## Prasinophyceae              1.122165e+00    0.497253391                NA
## Prasinophyceae_clade-IX     2.634064e-01    0.205670251         95.604396
## Prasinophyceae_clade-VII    5.268568e-01    0.325427612         95.604396
## Prymnesiophyceae            8.773618e-03    0.161412095         83.516484
## Pyramimonadaceae            2.484759e-03    0.007810263          7.692308
## Raphydophyceae              4.639682e-03    0.010413684         56.043956
## Trebouxiophyceae            2.264869e-03    0.007810263          4.395604
## Ulvophyceae                 3.518243e-04    0.007810263          4.395604
## other_Prasinophyceae        7.300353e-03    0.020827367         59.340659



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:


PHOTOTROPHS


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
##                                       59              1                NA
## Bacillariophyceae                   3636             98                88
## Bolidophyceae                       2971             15                89
## Chlorarachniophyceae                3335             70                89
## Chrysophyceae                      79873            361                91
## Cryptophyceae                       9910             77                80
## Dictyochophyceae                   39444            237                91
## Dinophyceae                       650673           9894                91
## Eustigmatales                        232              9                NA
## MOCH-1                              4357             70                NA
## MOCH-2                             17109            131                NA
## MOCH-5                              2431             19                NA
## Mamiellophyceae                      340             32                41
## Pelagophyceae                      46796            339                90
## Pinguiophyceae                      1544             19                86
## Prasinophyceae                     51033            191                NA
## Prasinophyceae_clade-IX            11979             79                87
## Prasinophyceae_clade-VII           23960            125                87
## Prymnesiophyceae                     399             62                76
## Pyramimonadaceae                     113              3                 7
## Raphydophyceae                       211              4                51
## Trebouxiophyceae                     103              3                 4
## Ulvophyceae                           16              3                 4
## other_Prasinophyceae                 332              8                54


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##               100               100                NA
##                          reads_per_class OTUs_per_class samples_per_class
##                              0.006204935    0.008438819                NA
## Bacillariophyceae            0.382392287    0.827004219         96.703297
## Bolidophyceae                0.312455303    0.126582278         97.802198
## Chlorarachniophyceae         0.350736599    0.590717300         97.802198
## Chrysophyceae                8.400115265    3.046413502        100.000000
## Cryptophyceae                1.042218801    0.649789030         87.912088
## Dictyochophyceae             4.148262197    2.000000000        100.000000
## Dinophyceae                 68.430235493   83.493670886        100.000000
## Eustigmatales                0.024399068    0.075949367                NA
## MOCH-1                       0.458218700    0.590717300                NA
## MOCH-2                       1.799326081    1.105485232                NA
## MOCH-5                       0.255664370    0.160337553                NA
## Mamiellophyceae              0.035757255    0.270042194         45.054945
## Pelagophyceae                4.921460242    2.860759494         98.901099
## Pinguiophyceae               0.162380003    0.160337553         94.505495
## Prasinophyceae               5.367058734    1.611814346                NA
## Prasinophyceae_clade-IX      1.259812211    0.666666667         95.604396
## Prasinophyceae_clade-VII     2.519834759    1.054852321         95.604396
## Prymnesiophyceae             0.041962190    0.523206751         83.516484
## Pyramimonadaceae             0.011884029    0.025316456          7.692308
## Raphydophyceae               0.022190531    0.033755274         56.043956
## Trebouxiophyceae             0.010832345    0.025316456          4.395604
## Ulvophyceae                  0.001682694    0.025316456          4.395604
## other_Prasinophyceae         0.034915907    0.067510549         59.340659



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:

1.6.2) Non-rarefied data


PHOTOTROPHS + HETEROTROPHS

No. of OTUs and reads of the rearefied dataset:

## [1] 43734
## [1] 12250242

No. of OTUs and reads of phototrophic groups:

## [1] 13555
## [1] 2515108

No. of OTUs and reads of non-phototrophic groups:

## [1] 30179
## [1] 9735134


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
##                                      150              1                NA
## Bacillariophyceae                   9195            109                89
## Bolidophyceae                       7156             16                89
## Chlorarachniophyceae               10036             80                89
## Chrysophyceae                     192835            418                91
## Cryptophyceae                      27260             95                81
## Dictyochophyceae                  104205            264                91
## Dinophyceae                      1769257          11319                91
## Eustigmatales                        573              9                NA
## Heterotrophs                     9735134          30179                91
## MOCH-1                             13716             83                NA
## MOCH-2                             45703            153                NA
## MOCH-5                              7015             25                NA
## Mamiellophyceae                      931             35                48
## Pelagophyceae                     121087            386                90
## Pinguiophyceae                      5296             27                89
## Prasinophyceae                    111285            218                NA
## Prasinophyceae_clade-IX            29715             86                87
## Prasinophyceae_clade-VII           56610            133                88
## Prymnesiophyceae                    1072             74                80
## Pyramimonadaceae                     254              3                 7
## Raphydophyceae                       664              4                62
## Trebouxiophyceae                     193              3                 4
## Ulvophyceae                           50              3                 5
## other_Prasinophyceae                 850             11                59


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##               100               100                NA
##                          reads_per_class OTUs_per_class samples_per_class
##                             1.224466e-03    0.002286551                NA
## Bacillariophyceae           7.505974e-02    0.249234006         97.802198
## Bolidophyceae               5.841517e-02    0.036584808         97.802198
## Chlorarachniophyceae        8.192491e-02    0.182924041         97.802198
## Chrysophyceae               1.574132e+00    0.955778113        100.000000
## Cryptophyceae               2.225262e-01    0.217222298         89.010989
## Dictyochophyceae            8.506363e-01    0.603649335        100.000000
## Dinophyceae                 1.444263e+01   25.881465222        100.000000
## Eustigmatales               4.677459e-03    0.020578955                NA
## Heterotrophs                7.946891e+01   69.005807838        100.000000
## MOCH-1                      1.119651e-01    0.189783692                NA
## MOCH-2                      3.730783e-01    0.349842228                NA
## MOCH-5                      5.726417e-02    0.057163763                NA
## Mamiellophyceae             7.599850e-03    0.080029268         52.747253
## Pelagophyceae               9.884458e-01    0.882608497         98.901099
## Pinguiophyceae              4.323180e-02    0.061736864         97.802198
## Prasinophyceae              9.084310e-01    0.498468011                NA
## Prasinophyceae_clade-IX     2.425666e-01    0.196643344         95.604396
## Prasinophyceae_clade-VII    4.621133e-01    0.304111218         96.703297
## Prymnesiophyceae            8.750848e-03    0.169204738         87.912088
## Pyramimonadaceae            2.073428e-03    0.006859652          7.692308
## Raphydophyceae              5.420301e-03    0.009146202         68.131868
## Trebouxiophyceae            1.575479e-03    0.006859652          4.395604
## Ulvophyceae                 4.081552e-04    0.006859652          5.494505
## other_Prasinophyceae        6.938638e-03    0.025152056         64.835165



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:


PHOTOTROPHS


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
##                                      150              1                NA
## Bacillariophyceae                   9195            109                89
## Bolidophyceae                       7156             16                89
## Chlorarachniophyceae               10036             80                89
## Chrysophyceae                     192835            418                91
## Cryptophyceae                      27260             95                81
## Dictyochophyceae                  104205            264                91
## Dinophyceae                      1769257          11319                91
## Eustigmatales                        573              9                NA
## MOCH-1                             13716             83                NA
## MOCH-2                             45703            153                NA
## MOCH-5                              7015             25                NA
## Mamiellophyceae                      931             35                48
## Pelagophyceae                     121087            386                90
## Pinguiophyceae                      5296             27                89
## Prasinophyceae                    111285            218                NA
## Prasinophyceae_clade-IX            29715             86                87
## Prasinophyceae_clade-VII           56610            133                88
## Prymnesiophyceae                    1072             74                80
## Pyramimonadaceae                     254              3                 7
## Raphydophyceae                       664              4                62
## Trebouxiophyceae                     193              3                 4
## Ulvophyceae                           50              3                 5
## other_Prasinophyceae                 850             11                59


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##               100               100                NA
##                          reads_per_class OTUs_per_class samples_per_class
##                              0.005963959    0.007377352                NA
## Bacillariophyceae            0.365590663    0.804131317         97.802198
## Bolidophyceae                0.284520585    0.118037624         97.802198
## Chlorarachniophyceae         0.399028590    0.590188122         97.802198
## Chrysophyceae                7.667066384    3.083732940        100.000000
## Cryptophyceae                1.083850077    0.700848395         89.010989
## Dictyochophyceae             4.143162043    1.947620804        100.000000
## Dinophyceae                 70.345170068   83.504241977        100.000000
## Eustigmatales                0.022782322    0.066396164                NA
## MOCH-1                       0.545344375    0.612320177                NA
## MOCH-2                       1.817138668    1.128734784                NA
## MOCH-5                       0.278914464    0.184433788                NA
## Mamiellophyceae              0.037016303    0.258207304         52.747253
## Pelagophyceae                4.814385704    2.847657691         98.901099
## Pinguiophyceae               0.210567498    0.199188491         97.802198
## Prasinophyceae               4.424660889    1.608262634                NA
## Prasinophyceae_clade-IX      1.181460200    0.634452232         95.604396
## Prasinophyceae_clade-VII     2.250797978    0.981187754         96.703297
## Prymnesiophyceae             0.042622424    0.545924013         87.912088
## Pyramimonadaceae             0.010098970    0.022132055          7.692308
## Raphydophyceae               0.026400457    0.029509406         68.131868
## Trebouxiophyceae             0.007673627    0.022132055          4.395604
## Ulvophyceae                  0.001987986    0.022132055          5.494505
## other_Prasinophyceae         0.033795765    0.081150867         64.835165



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:





OLD VERSION

1.6) Taxonomic composition analysis

1.6.1) Normalized data

1.6.1.1) Absolute values

Let’s add the taxonomic classification by merging “tb18_tax_occur_ss49975_no_cero” with “tb18_tax”:

## [1] 38411    99
##   Row.names st001_MD28 st002_MD40 st003_MD52 st005_MD64
## 1     OTU_1        158        136        236        155
## 2    OTU_10          4         49        167         75
## 3   OTU_100         72        221         25         49
## 4  OTU_1000          1          0          8          0
## 5 OTU_10000          1          3          5          0
## [1] 38411    98
##           st001_MD28 st002_MD40 st003_MD52 st005_MD64 st009_MD111
## OTU_1            158        136        236        155         222
## OTU_10             4         49        167         75          84
## OTU_100           72        221         25         49         358
## OTU_1000           1          0          8          0           0
## OTU_10000          1          3          5          0           0
## [1] 38411    99
##       st001_MD28 st002_MD40 st003_MD52 st005_MD64 st009_MD111
## OTU_1        158        136        236        155         222
## OTU_2        154        249        733        847        2212
## OTU_3        350       1481       1571        434         289
## OTU_4         44         45         32        125          94
## OTU_5          0        126        273         45         101
## [1] 11850    99
#create a table per group and count in how many samples they occur. 
Dinophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Dinophyceae"),]
Dinophyceae_tb[1:5,1:5]
##      st001_MD28 st002_MD40 st003_MD52 st005_MD64 st009_MD111
## NA           NA         NA         NA         NA          NA
## NA.1         NA         NA         NA         NA          NA
## NA.2         NA         NA         NA         NA          NA
## NA.3         NA         NA         NA         NA          NA
## NA.4         NA         NA         NA         NA          NA
Dinophyceae_tb_occur <- Dinophyceae_tb[,1:91]
Dinophyceae_tb_occur[1:5,1:5]
##      st001_MD28 st002_MD40 st003_MD52 st005_MD64 st009_MD111
## NA           NA         NA         NA         NA          NA
## NA.1         NA         NA         NA         NA          NA
## NA.2         NA         NA         NA         NA          NA
## NA.3         NA         NA         NA         NA          NA
## NA.4         NA         NA         NA         NA          NA
dim(Dinophyceae_tb_occur)
## [1]  0 91
length(Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0])
## [1] 0
#Dinophyceae_tb_samples <- Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0]
#length(Dinophyceae_tb_samples[which(colSums(Dinophyceae_tb_occur) != 0)])

Prasinophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "other_Prasinophyceae"),]
Prasinophyceae_tb_occur <- Prasinophyceae_tb[,1:91]
length(Prasinophyceae_tb_occur[,colSums(Prasinophyceae_tb_occur) > 0])
## [1] 0
Chrysophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Chrysophyceae"),]
Chrysophyceae_tb_occur <- Chrysophyceae_tb[,1:91]
length(Chrysophyceae_tb_occur[,colSums(Chrysophyceae_tb_occur) > 0])
## [1] 0
Pelagophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Pelagophyceae"),]
Pelagophyceae_tb_occur <- Pelagophyceae_tb[,1:91]
length(Pelagophyceae_tb_occur[,colSums(Pelagophyceae_tb_occur) > 0])
## [1] 0
Dictyochophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Dictyochophyceae"),]
Dictyochophyceae_tb_occur <- Dictyochophyceae_tb[,1:91]
length(Dictyochophyceae_tb_occur[,colSums(Dictyochophyceae_tb_occur) > 0])
## [1] 0
Cryptomonadales_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Cryptophyceae"),]
Cryptomonadales_tb_occur <- Cryptomonadales_tb[,1:91]
length(Cryptomonadales_tb_occur[,colSums(Cryptomonadales_tb_occur) > 0])
## [1] 0
Bacillariophyta_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Bacillariophyceae"),]
Bacillariophyta_tb_occur <- Bacillariophyta_tb[,1:91]
length(Bacillariophyta_tb_occur[,colSums(Bacillariophyta_tb_occur) > 0])
## [1] 0
Chlorarachniophyta_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Chlorarachniophyceae"),]
Chlorarachniophyta_tb_occur <- Chlorarachniophyta_tb[,1:91]
length(Chlorarachniophyta_tb_occur[,colSums(Chlorarachniophyta_tb_occur) > 0])
## [1] 0
Bolidophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Bolidophyceae"),]
Bolidophyceae_tb_occur <- Bolidophyceae_tb[,1:91]
length(Bolidophyceae_tb_occur[,colSums(Bolidophyceae_tb_occur) > 0])
## [1] 0
Pinguiochysidales_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Pinguiophyceae"),]
Pinguiochysidales_tb_occur <- Pinguiochysidales_tb[,1:91]
length(Pinguiochysidales_tb_occur[,colSums(Pinguiochysidales_tb_occur) > 0])
## [1] 0
Prymnesiophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Prymnesiophyceae"),]
Prymnesiophyceae_tb_occur <- Prymnesiophyceae_tb[,1:91]
length(Prymnesiophyceae_tb_occur[,colSums(Prymnesiophyceae_tb_occur) > 0])
## [1] 0
Mamiellophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Mamiellophyceae"),]
Mamiellophyceae_tb_occur <- Mamiellophyceae_tb[,1:91]
length(Mamiellophyceae_tb_occur[,colSums(Mamiellophyceae_tb_occur) > 0])
## [1] 0
Eustigmatales_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Eustigmatophyceae"),]
Eustigmatales_tb_occur <- Eustigmatales_tb[,1:91]
length(Eustigmatales_tb_occur[,colSums(Eustigmatales_tb_occur) > 0])
## [1] 0
Chlorophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Chlorophyceae"),]
Chlorophyceae_tb_occur <- Chlorophyceae_tb[,1:91]
length(Chlorophyceae_tb_occur[,colSums(Chlorophyceae_tb_occur) > 0])
## [1] 0
Ulvophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Ulvophyceae"),]
Ulvophyceae_tb_occur <- Ulvophyceae_tb[,1:91]
length(Ulvophyceae_tb_occur[,colSums(Ulvophyceae_tb_occur) > 0])
## [1] 0
Raphydophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Raphydophyceae"),]
Raphydophyceae_tb_occur <- Raphydophyceae_tb[,1:91]
length(Raphydophyceae_tb_occur[,colSums(Raphydophyceae_tb_occur) > 0])
## [1] 0
Trebouxiophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Trebouxiophyceae"),]
Trebouxiophyceae_tb_occur <- Trebouxiophyceae_tb[,1:91]
length(Trebouxiophyceae_tb_occur[,colSums(Trebouxiophyceae_tb_occur) > 0])
## [1] 0
Phaeophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Phaeophyceae"),]
Phaeophyceae_tb_occur <- Phaeophyceae_tb[,1:91]
length(Phaeophyceae_tb_occur[,colSums(Phaeophyceae_tb_occur) > 0])
## [1] 0
Phaeothamniophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Phaeothamniophyceae"),]
Phaeothamniophyceae_tb_occur <- Phaeothamniophyceae_tb[,1:91]
length(Phaeothamniophyceae_tb_occur[,colSums(Phaeothamniophyceae_tb_occur) > 0])
## [1] 0
Xanthophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Xanthophyceae"),]
Xanthophyceae_tb_occur <- Xanthophyceae_tb[,1:91]
length(Xanthophyceae_tb_occur[,colSums(Xanthophyceae_tb_occur) > 0])
## [1] 0
Chlorodendrophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Chlorodendrophyceae"),]
Chlorodendrophyceae_tb_occur <- Chlorodendrophyceae_tb[,1:91]
length(Chlorodendrophyceae_tb_occur[,colSums(Chlorodendrophyceae_tb_occur) > 0])
## [1] 0
IncertaeSedis_Archaeplastida_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "IncertaeSedis_Archaeplastida"),]
IncertaeSedis_Archaeplastida_tb_occur <- IncertaeSedis_Archaeplastida_tb[,1:91]
length(IncertaeSedis_Archaeplastida_tb_occur[,colSums(IncertaeSedis_Archaeplastida_tb_occur) > 0])
## [1] 0
Nephroselmidophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Nephroselmidophyceae"),]
Nephroselmidophyceae_tb_occur <- Nephroselmidophyceae_tb[,1:91]
length(Nephroselmidophyceae_tb_occur[,colSums(Nephroselmidophyceae_tb_occur) > 0])
## [1] 0
Pavlovophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Pavlovophyceae"),]
Pavlovophyceae_tb_occur <- Pavlovophyceae_tb[,1:91]
length(Pavlovophyceae_tb_occur[,colSums(Pavlovophyceae_tb_occur) > 0])
## [1] 0
Rhodophyceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Rhodophyceae"),]
Rhodophyceae_tb_occur <- Rhodophyceae_tb[,1:91]
length(Rhodophyceae_tb_occur[,colSums(Rhodophyceae_tb_occur) > 0])
## [1] 0
Rappemonads_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Rappemonads"),]
Rappemonads_tb_occur <- Rappemonads_tb[,1:91]
length(Rappemonads_tb_occur[,colSums(Rappemonads_tb_occur) > 0])
## [1] 0
MOCH_1_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "MOCH-1"),]
MOCH_1_tb_occur <- MOCH_1_tb[,1:91]
length(MOCH_1_tb_occur[,colSums(MOCH_1_tb_occur) > 0])
## [1] 0
MOCH_2_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "MOCH-2"),]
MOCH_2_tb_occur <- MOCH_2_tb[,1:91]
length(MOCH_2_tb_occur[,colSums(MOCH_2_tb_occur) > 0])
## [1] 0
MOCH_5_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "MOCH-5"),]
MOCH_5_tb_occur <- MOCH_5_tb[,1:91]
length(MOCH_5_tb_occur[,colSums(MOCH_5_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_VII_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Prasinophyceae_clade-VII"),]
Prasinophyceae_clade_VII_tb_occur <- Prasinophyceae_clade_VII_tb[,1:91]
length(Prasinophyceae_clade_VII_tb_occur[,colSums(Prasinophyceae_clade_VII_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_IX_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Prasinophyceae_clade-IX"),]
Prasinophyceae_clade_IX_tb_occur <- Prasinophyceae_clade_IX_tb[,1:91]
length(Prasinophyceae_clade_IX_tb_occur[,colSums(Prasinophyceae_clade_IX_tb_occur) > 0])
## [1] 0
Pyramimonadaceae_tb <- tb18_phototrophs[which(tb18_phototrophs$classif == "Pyramimonadaceae"),]
Pyramimonadaceae_tb_occur <- Pyramimonadaceae_tb[,1:91]
length(Pyramimonadaceae_tb_occur[,colSums(Pyramimonadaceae_tb_occur) > 0])
## [1] 0
##                      reads_per_class OTUs_per_class
## Bacillariophyceae               3636             98
## Bolidophyceae                   2971             15
## Chlorarachniophyceae            3335             70
## Chrysophyceae                  79873            361
## Cryptophyceae                   9910             77
##                          reads_per_class OTUs_per_class samples_per_class
## Dinophyceae                       650673           9894                 0
## Chrysophyceae                      79873            361                 0
## Prasinophyceae                     51033            191                 0
## Pelagophyceae                      46796            339                 0
## Dictyochophyceae                   39444            237                 0
## Prasinophyceae_clade-VII           23960            125                 0
## MOCH-2                             17109            131                 0
## Prasinophyceae_clade-IX            11979             79                 0
## Cryptophyceae                       9910             77                 0
## MOCH-1                              4357             70                 0
## Bacillariophyceae                   3636             98                 0
## Chlorarachniophyceae                3335             70                 0
## Bolidophyceae                       2971             15                 0
## MOCH-5                              2431             19                 0
## Pinguiophyceae                      1544             19                 0
## Prymnesiophyceae                     399             62                 0
## Mamiellophyceae                      340             32                 0
## other_Prasinophyceae                 332              8                 0
## Eustigmatales                        232              9                 0
## Raphydophyceae                       211              4                 0
## Pyramimonadaceae                     113              3                 0
## Trebouxiophyceae                     103              3                 0
## Ulvophyceae                           16              3                 0

1.6.1.2) Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##               100               100                 0
##                          reads_per_class OTUs_per_class samples_per_class
## Dinophyceae                 68.434481808    83.50071736                 0
## Chrysophyceae                8.400636519     3.04667061                 0
## Prasinophyceae               5.367391778     1.61195038                 0
## Pelagophyceae                4.921765635     2.86100093                 0
## Dictyochophyceae             4.148519610     2.00016879                 0
## Prasinophyceae_clade-VII     2.519991123     1.05494135                 0
## MOCH-2                       1.799437735     1.10557853                 0
## Prasinophyceae_clade-IX      1.259890387     0.66672293                 0
## Cryptophyceae                1.042283474     0.64984387                 0
## MOCH-1                       0.458247134     0.59076715                 0
## Bacillariophyceae            0.382416015     0.82707401                 0
## Chlorarachniophyceae         0.350758364     0.59076715                 0
## Bolidophyceae                0.312474692     0.12659296                 0
## MOCH-5                       0.255680235     0.16035108                 0
## Pinguiophyceae               0.162390079     0.16035108                 0
## Prymnesiophyceae             0.041964794     0.52325091                 0
## Mamiellophyceae              0.035759473     0.27006498                 0
## other_Prasinophyceae         0.034918074     0.06751625                 0
## Eustigmatales                0.024400582     0.07595578                 0
## Raphydophyceae               0.022191908     0.03375812                 0
## Pyramimonadaceae             0.011884766     0.02531859                 0
## Trebouxiophyceae             0.010833017     0.02531859                 0
## Ulvophyceae                  0.001682799     0.02531859                 0



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:

1.6.2) Non-normalized data

## [1] 43734    99
##   Row.names st055_MD1013 st057_MD1042 st058_MD1080 st059_MD1100
## 1     OTU_1          579         5968         2609         1500
## 2    OTU_10           26            5            1           26
## 3   OTU_100           31          159           21            8
## 4  OTU_1000            0           95           26           21
## 5 OTU_10000            0            0            0            0
## [1] 43734    98
##           st055_MD1013 st057_MD1042 st058_MD1080 st059_MD1100 st009_MD111
## OTU_1              579         5968         2609         1500         815
## OTU_10              26            5            1           26         309
## OTU_100             31          159           21            8        1340
## OTU_1000             0           95           26           21           0
## OTU_10000            0            0            0            0           0
## [1] 43734    99
##       st055_MD1013 st057_MD1042 st058_MD1080 st059_MD1100 st009_MD111
## OTU_1          579         5968         2609         1500         815
## OTU_2         9289        16285         5140         1187        8207
## OTU_3           15           96           18            6        1061
## OTU_4          230          776          150          561         337
## OTU_5           68          513          287          604         396
## [1] 13554    99
##        st055_MD1013 st057_MD1042 st058_MD1080 st059_MD1100 st009_MD111
## OTU_1           579         5968         2609         1500         815
## OTU_4           230          776          150          561         337
## OTU_18         1042         4241         5755         3019        1129
## OTU_25         1353         6434         4523         4370        3060
## OTU_33          185          745         1559          258         615
##        st055_MD1013 st057_MD1042 st058_MD1080 st059_MD1100 st009_MD111
## OTU_1           579         5968         2609         1500         815
## OTU_4           230          776          150          561         337
## OTU_18         1042         4241         5755         3019        1129
## OTU_25         1353         6434         4523         4370        3060
## OTU_33          185          745         1559          258         615
## [1] 11319    91
## [1] 91
## [1] 91
## [1] 91
## [1] 91
## [1] 90
## [1] 91
## [1] 0
## [1] 0
## [1] 0
## [1] 89
## [1] 0
## [1] 80
## [1] 48
## [1] 31
## [1] 0
## [1] 5
## [1] 62
## [1] 4
##                     Group.1       x
## 7               Dinophyceae 1769257
## 4             Chrysophyceae  192835
## 13            Pelagophyceae  121087
## 15           Prasinophyceae  111285
## 6          Dictyochophyceae  104205
## 17 Prasinophyceae_clade-VII   56610
## 10                   MOCH-2   45703
## 16  Prasinophyceae_clade-IX   29715
## 5             Cryptophyceae   27260
## 9                    MOCH-1   13716
## 3      Chlorarachniophyceae   10036
## 1         Bacillariophyceae    9195
## 2             Bolidophyceae    7156
## 11                   MOCH-5    7015
## 14           Pinguiophyceae    5296
## 18         Prymnesiophyceae    1072
## 12          Mamiellophyceae     931
## 23     other_Prasinophyceae     850
## 20           Raphydophyceae     664
## 8             Eustigmatales     573
## 19         Pyramimonadaceae     254
## 21         Trebouxiophyceae     193
## 22              Ulvophyceae      50
##                     Group.1     x
## 7               Dinophyceae 11319
## 4             Chrysophyceae   418
## 13            Pelagophyceae   386
## 6          Dictyochophyceae   264
## 15           Prasinophyceae   218
## 10                   MOCH-2   153
## 17 Prasinophyceae_clade-VII   133
## 1         Bacillariophyceae   109
## 5             Cryptophyceae    95
## 16  Prasinophyceae_clade-IX    86
## 9                    MOCH-1    83
## 3      Chlorarachniophyceae    80
## 18         Prymnesiophyceae    74
## 12          Mamiellophyceae    35
## 14           Pinguiophyceae    27
## 11                   MOCH-5    25
## 2             Bolidophyceae    16
## 23     other_Prasinophyceae    11
## 8             Eustigmatales     9
## 20           Raphydophyceae     4
## 19         Pyramimonadaceae     3
## 21         Trebouxiophyceae     3
## 22              Ulvophyceae     3
##                      reads_per_class OTUs_per_class
## Bacillariophyceae               9195            109
## Bolidophyceae                   7156             16
## Chlorarachniophyceae           10036             80
## Chrysophyceae                 192835            418
## Cryptophyceae                  27260             95
##                          reads_per_class OTUs_per_class samples_per_class
## Dinophyceae                      1769257          11319                92
## Chrysophyceae                     192835            418                92
## Pelagophyceae                     121087            386                92
## Prasinophyceae                    111285            218               113
## Dictyochophyceae                  104205            264               116
## Prasinophyceae_clade-VII           56610            133               103
## MOCH-2                             45703            153               112
## Prasinophyceae_clade-IX            29715             86               112
## Cryptophyceae                      27260             95               108
## MOCH-1                             13716             83               111
## Chlorarachniophyceae               10036             80                97
## Bacillariophyceae                   9195            109                65
## Bolidophyceae                       7156             16                35
## MOCH-5                              7015             25                75
## Pinguiophyceae                      5296             27                75
## Prymnesiophyceae                    1072             74                50
## Mamiellophyceae                      931             35                18
## other_Prasinophyceae                 850             11                 1
## Raphydophyceae                       664              4                 1
## Eustigmatales                        573              9                 1
## Pyramimonadaceae                     254              3                 1
## Trebouxiophyceae                     193              3                 1
## Ulvophyceae                           50              3                 1
##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1617.582
##                          reads_per_class OTUs_per_class samples_per_class
## Dinophyceae                 70.349365675    83.51040283        101.098901
## Chrysophyceae                7.667523672     3.08396045        101.098901
## Pelagophyceae                4.814672849     2.84786779        101.098901
## Prasinophyceae               4.424924790     1.60838129        124.175824
## Dictyochophyceae             4.143409154     1.94776450        127.472527
## Prasinophyceae_clade-VII     2.250932222     0.98126014        113.186813
## MOCH-2                       1.817247047     1.12881806        123.076923
## Prasinophyceae_clade-IX      1.181530666     0.63449904        123.076923
## Cryptophyceae                1.083914721     0.70090010        118.681319
## MOCH-1                       0.545376901     0.61236535        121.978022
## Chlorarachniophyceae         0.399052390     0.59023167        106.593407
## Bacillariophyceae            0.365612467     0.80419064         71.428571
## Bolidophyceae                0.284537555     0.11804633         38.461538
## MOCH-5                       0.278931099     0.18444740         82.417582
## Pinguiophyceae               0.210580057     0.19920319         82.417582
## Prymnesiophyceae             0.042624966     0.54596429         54.945055
## Mamiellophyceae              0.037018511     0.25822635         19.780220
## other_Prasinophyceae         0.033797781     0.08115685          1.098901
## Raphydophyceae               0.026402031     0.02951158          1.098901
## Eustigmatales                0.022783681     0.06640106          1.098901
## Pyramimonadaceae             0.010099572     0.02213369          1.098901
## Trebouxiophyceae             0.007674084     0.02213369          1.098901
## Ulvophyceae                  0.001988105     0.02213369          1.098901

Reads per class vs. OTUs per class:



Reads OTUs per class vs. samples in which they occurr: